The Project Freelancer Saga is the third main saga of the series, spanning two seasons and two mini-series. Unlike the previous two sagas, however, the Project Freelancer saga focuses on prequel events taking place before The Blood Gulch Chronicles, as well as present day events. The saga is notable for its extensive use of original character animation, first introduced in Revelation, allowing for more intricate action sequences, unique character designs, and a better use of visual storytelling. The saga also wraps up several elements introduced in the previous two sagas.

Where There's a Will, There's a Wall is a mini-series, taking place inside the Epsilon Unit, that follows the Red Team discovering a huge wall behind their base. Meanwhile, the Blues rejoice over their newly arrived Falcon and argue to see who gets control over it.

The tenth season continues after the events of Season 9, following Carolina's journey to kill the Director with the Reds and Blues, as well as wrapping up the events of the Freelancer backstory, first introduced in Season 9. This season also elaborates more on the Freelancer A.I. fragments.

Epsilon is obsessed with getting Epsilon Tex out of the memory unit. The Director is obsessed with reviving Allison though Tex and torturing the Alpha A.I to create fragments. Carolina is obsessed with defeating Tex and impressing and later killing her father the Director. Sigma is obsessed with collecting his fellow fragments and obtaining metastability. South is obsessed with obtaining an A.I.

Though the two seasons particularly the 10th we see the director's inability to let go of Allison and how his inability to let go drives him to do morally horrible things to try to bring her back. In the end, we see how his unwillingness to let go has caused the destruction of so much else he cared for and left him a shell of his former self. Epsilon realizes his only way to be happy is let go of his memory of her. Towards the end, we see Carolina and Epsilon manage to let go of their hate for the director and rather than kill him, they decide to leave him alone to decide his own fate.